Ooooooo.... here we go
(Thank you, tjw, for having different numbers of steps for the different platforms so I don't have to ask.)
You change directories using the "cd" command. So if you put tremded.exe at C:\Program Files\Tremulous\tremded.exe, you would enter at the command prompt
cd C:\Program Files\Tremulous\
and the prompt should change to
C:\Program Files\Tremulous\>
then run tremded using the exact string below "run it:". So before pressing enter, the line should look something like
C:\Program Files\Tremulous\> tremded.exe +set dedicated 2 +exec settings.cfg